Any tools for RNA graph?

Yushan Hsiao · 01-03-2011, 11:47 PM

I need to draw the secondary structure of small RNA precursors.
Is there any tool that could produce many graphs at a time when I give it the all the sequences or parenthesis of RNAfold?

Besides, I also want to mark the specific sequence on the graph of my RNA structure. I saw some paper with red letters on the graph to point them out, but I don't know how do they produce this result?

Could anyone help? Thanks a lot.

ppgardne · 01-04-2011, 01:24 AM

VARNA is quite good. Lots of different layouts are possible.

The Vienna package ships with RNAplot which will ps & svg. RNAfold usually generates a postscript (rna.ps) by default. There are some scripts for manipulating the Vienna ps files in your ViennaRNA-1.x.x/Utils/ directory.

ppgardne · 01-10-2011, 01:04 AM

R2R has just been published. It also produces some very nice graphics:
http://www.biomedcentral.com/1471-2105/12/3

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01-03-2011, 11:47 PM	#1
Yushan Hsiao Junior Member Location: Taiwan Join Date: Aug 2010 Posts: 6	Any tools for RNA graph? I need to draw the secondary structure of small RNA precursors. Is there any tool that could produce many graphs at a time when I give it the all the sequences or parenthesis of RNAfold? Besides, I also want to mark the specific sequence on the graph of my RNA structure. I saw some paper with red letters on the graph to point them out, but I don't know how do they produce this result? Could anyone help? Thanks a lot.

01-04-2011, 01:24 AM	#2
ppgardne Member Location: New Zealand Join Date: Oct 2010 Posts: 13	VARNA is quite good. Lots of different layouts are possible. The Vienna package ships with RNAplot which will ps & svg. RNAfold usually generates a postscript (rna.ps) by default. There are some scripts for manipulating the Vienna ps files in your ViennaRNA-1.x.x/Utils/ directory.

01-10-2011, 01:04 AM	#3
ppgardne Member Location: New Zealand Join Date: Oct 2010 Posts: 13	R2R has just been published. It also produces some very nice graphics: http://www.biomedcentral.com/1471-2105/12/3